We have previously described the isolation of a novel enhancer-binding protein fraction from transformed human and mouse cells. The isolated fraction, designated EBP-80, consisted of two proteins of 70 and 85kD and acted to stimulate promoter activity of IAP LTRs in a cell-free transcription system. During the past year, a quantity of highly purified EBP-80 was isolated from human 293 (adeno-transformed) cells and the two components separated in quantities sufficient for micro-sequencing. Amino acid analysis of tryptic peptides established that both components of EBP-80 are identical to those in a human protein, called Ku, previously identified as an autoantigen in several human disorders (autoimmune thyroiditis, disseminated lupus, and others). cDNAs for both components have been cloned and sequenced in other laboratories. Ku binds to the ends of duplex DNAs and has been suggested to have a role in recombination or DNA repair. Ku-like preparations have also been isolated as transcription and/or DNA-binding factors from several other genes. Ku is reported not to bind to circular DNA. However, our own analysis shows that EBP-80/Ku does bind to closed circular templates under the buffer conditions for in vitro transcription. In addition, we have developed evidence that EBP-80 can bind to internal transitions between double- and single-stranded DNA, as would occur in regions of DNA unwinding or palindromic stem-loop extensions. Both of these configurations have been implicated in transcriptional regulation. IAP expression in normal mouse thymus is under genetic control, since thymocytes from different inbred strains differed characteristically in the level and proportion of IAP transcripts. Thymus and LPS-stimulated splenic B cells of BALB/cAn mice contain limited and largely overlapping sets of IAP transcripts: 13 highly related IAP elements are responsible for most of the expression in these cells. Analysis of primary myelomas shows that hypomethylation and expression of IAP elements is an early event in development of these B-cell tumors.